User:Eric Martz/Sandbox 4

Running State Script

This green link is a <jmolLink> that directly loads an uploaded script (a modified state script). When the script is dropped into Jmol.jar 14.31.8 (current main version in Proteopedia) it works (3 unrecognized but harmless set commands) even though the script was written from JSmol 14.32.64.

The load command in the script loads a "frozen" uploaded PDB file Image:1sva-revdat2009.pdb.gz.

Changes to the state script:

1. load command should load frozen uploaded .pdb.gz file, for example Image:1sva-revdat2009.pdb.gz.
2. Optional: delete the DATA block in _setDataState()
3. Caption in _setState(), see 1sva-half-capsid-distance3.spt.

JSmol Version

The state script was generated by JSmol 14.32.64.

The load command in the script includes FILTER "*.CA;biomolecule 1;bmchains;/=5".

Filters "*.CA;biomolecule 1;" and "/=5" work in JSmol 14.31.8. Filter "bmchains" is ignored, so all copies of chain "1" are also named "1". This does not matter.

As long as the atomindex values generated in 14.31.8 match those generated in 14.32.64, the script works. The script does not work if ligand HETATM are present in the AU because new JSmol includes them in BU1 while old JSmol does not. Therefore the scene must be generated in FirstGlance from an AU PDB file from which ligand HETATM have been deleted, and that PDB file must be uploaded for use by Proteopedia, e.g. 6mx4-nohet.pdb.gz.

TEST OF NOHET SOLUTION

Scenes Saved from the SAT

FAILS BECAUSE CAPTION CONTAINS SEMICOLON: : Scene created by dropping half-capsid-nodata.spt into JSmol after first loading 1sva. State script load command modified to load "" FILTER "*.CA;biomolecule 1;bmchains;/=5"; and function _setDataState() made an empty function {} (previously it assigned distances from center to each of ~25,000 alpha carbons).

.

Scene 85/859610/1ijw/1 is wiki/scripts/85/859610/1ijw/1.spt

Within function _setState():

ppdiaCaptionCmd = "changeCaption('This is test caption XXX.','white','black');";
 javascript @ppdiaCaptionCmd;

.

Echos 1SVA but no atoms appear. Loads only 15K atoms instead of 24K.